Hey, I am building a phylogenetic tree of the Anoctamin family including a candidate gene from C.intestinalis (tunciate). A blast in the Aniseed (Ciona) database gave no name for this gene, just that it's closest blast hits in humans were Ano3, Ano4 and Ano5, so I called my gene Ci-Ano3/4/5.

When building a phylogeny of the whole gene family, my gene Ci-Ano3/4/5 falls just outside a clade with vertebrate paralogs Ano3, Ano4 and Ano9 (the clade containing Ano5/6 diverged earlier)

Does this mean I should rename my gene Ci-Ano3/4/9 even though there is no info in any gene database I can find which gives it this name (Ensembl and NCBI both call it Ci-Ano5)?

If so, then Ensembl already knows about Anoctamin orthologs and this would be the authoritative source for the recent genome annotation. Ensembl calls them simply 'anoctamin'. The numbers are not that relevant because they are used to number the paralogs in one organism. If Ciona has 3 paralogs and human has 10, it doesn't make too much sense to name a Ciona gene Ano2/4/9 (that looks like there were 9 Ciona paralogs). If you are not sure, and also Ensembl Compara has not picked up this ortholog, I'd annotate "Hypothetical protein, anoctamin-like", "Anoctamin-like protein" or "Similar to Anocatamin2 [homo sapiens]".

While vertebrates have 10 paralogs, most other organisms contain three or four anoctamin family members.[...]

In each of the urochordata genomes, Ciona inestinalis and Ciona savigny, the closest relatives of the craniates, we identified three anoctamin sequences. Thus, gene duplication of the anoctamin family appeared to have occurred very early at the base of the chordates tree.